As my textbook An Introduction to Genetic Analysis points out, yeast mitochondrial DNA has approximately 78 kb of genetic data, while the human mitochondrial DNA contains 17 kb. Is there any evolution reason for this drastic change in size? Also, are there any particularities about mitochondrial function that have been compromised with this reduction in size?

I know yeast is supposed to have very little non-coding DNA, but could it be possible that mitochondria in yeast have more intron regions?
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Ultimate GobblementFeb 14 '12 at 20:25

There is a diagram showing the decrease in intron regions for humans. Nonetheless, could the sole evolutionary reason for the decrease be that it's simply more efficient in replication, or the efficiency of use of nucleic acids?
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LanceLafontaineFeb 14 '12 at 20:30

I think that to look at the evolutionary aspect of this question fairly, one needs to consider many other organisms in addition to human and brewer's yeast. An alignment of the genomes, or perhaps a simple list of the encoded genes will address the question of compromising of function with changes in genome size.
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Larry_ParnellMar 13 '12 at 20:21

2 Answers
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One of the contributing factors the size of the yeast mitochondrial genome are 'selfish' mobile genetic elements termed homing endonucleases genes (HEGs). These genes are typically found in introns that encode site-specific DNA endonucleases. These endnoclueases cleave the HEG- alleles during yeast mating leading to DNA recombination using the HEG+ allele as template. I suspect over time as organisms became more complex and HEGs become unable to mobilize they would become fixed in the organisms genome. Upon being fixed there is no selection pressure to maintain the open reading frame of the HEG or the intron its encoded within (ref). This causes the eventual loss of the HEG and intron since they provide no real benefit to the organisms genome.

I don't know how much of the yeast mitochondrial genome is taken up by these introns. I believe that there are 4 of them in yeast some of the introns also require reverse transcriptase for splicing and mobility. Other fungal species can have many more introns and sometimes weird things like introns embedded within introns.

Shorter DNA would allows easier synthesis, but more introns could allow for more different transcription factors to influence gene expression.

Human mitochondria probably does not need to be as adaptable as mitochondria in yeast, since the a human cell's environment tends to be more stable. This could provide a viable reason as to why human mitochondria does not need as many introns, but this is only how I imagine things. I have no proof or experience to validate any of this - its just a possiblility.